Genetic association analysis of rare variants is an area of growing importance in genetics. Rare variants may explain a large portion of the tieritability that has not been explained by common variants, and will lead to new insights into the aetiology of common diseases. Increasing amounts of sequence data are being generated in order to investigate rare variants; however, statistical methods for analysis of these data are in their infancy. We will develop statistical methodology to leverage genome-wide association data for rare variant analysis through imputation, haplotypic testing and selection of samples for sequencing, and we will compare methods for rare variant association analysis. We will also develop statistical methodology to detect population structure and correct for it in association analysis, with a particular focus on rare variant analysis.